DNA templated nucleophilic aromatic substitution reactions for fluorogenic sensing of oligonucleotides

Abstract

We have developed an S(N)Ar reaction-triggered fluorescence probe using a new fluorogenic compound derivatized from 7-aminocoumarin for oligonucleotides detection.

Two Successive Reactions on a DNA Template: A Strategy for Improving Background Fluorescence and Specificity in Nucleic Acid Detection

“…To improve the characteristics of template-mediated fluorescence activation schemes, several groups have investigated varied chemical reactions and fluorescence turn-on strategies for the detection of nucleic acids in vitro [8] and in cells. [7,9] One recent probe design that has displayed promise in engendering low background and high sequence-specificity is that of quenched Staudinger reaction-triggered α-azidoether release probes (Q-STAR probes).…”

Coumarin-Derived Fluorescent Chemosensors

“…Coumarin 6 has been used as a fluorescent probe to monitor protein aggregation and can distinguish between both amorphors and fibrillar aggregates (Makwana et al, 2011). An S N Ar reaction-triggered fluorescence probe is developed using a new fluorogenic compound derivatized from 7-aminocoumarin for oligonucleotides detection (Shibata et al, 2009). Coumarin C343 has been conjugated to silica nanoparticles and entrapped in a sol-gel matrix to produce a nanosensor capable of monitoring lipid peroxidation (Baker et al, 2007).…”

Dual Sensing of Hairpin and Quadruplex DNA Structures Using Multicolored Peptide Nucleic Acid Fluorescent Probes

“…The system has been designed such that the Cy5 product forms solely upon simultaneous hybridization of both probes to either the loop or the stem of a unique hairpin DNA target. Therefore, hairpin formation will be directly linked to the appearance of a fluorescent signal at long wavelength (λ em > 650 nm), well above the residual fluorescence of biological media, and above the fluorescence emission wavelength of most fluorescent products formed in oligonucleotide-templated reactions, (21)(22)(23)(24)(25)(26)(27)(28)(29) including that previously reported by us (27). Simultaneous sensing of various DNA structures via a two-color (Cy3-Cy5) system will also be presented.…”

“…A characteristic fluorescent signal will then be emitted which can be directly linked to the detection of the targeted sequence and/or structure. (20) Most recent reports of DNA-templated reactions applied to oligonucleotide sensing are based on the Staudinger reaction, (21)(22)(23)(24)(25) aldol-type, (26)(27) organomercury-activated (28) or S N Ar (29) reactions.…”